{"ID": "PMID:40082674", "aka": "http://biorxiv.org/lookup/doi/10.1101/2024.05.16.594268", "lab": {"display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/40082674", "award": {"uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "project": "4DN", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "name": "2U01CA200059-06", "@id": "/awards/2U01CA200059-06/", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "center_title": "DCIC - Park", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection  of chromatin loops and stripes.", "status": "current", "aliases": ["4dn-dcic-lab:buka_plewcynski_hichip_pub_pmid40082674"], "authors": ["Buka K", "Parteka-Tojek Z", "Agarwal A", "Denkiewicz M", "Korsak S", "Chilinski M", "Banecki KH", "Plewczynski D"], "journal": "Communications biology", "abstract": "Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput  variation of 3 C), detect pairwise interactions between DNA regions, enabling the  reconstruction of chromatin architecture in the nucleus. HiChIP is a modification  of the Hi-C experiment that includes a chromatin immunoprecipitation (ChIP) step,  allowing genome-wide identification of chromatin contacts mediated by a protein  of interest. In mammalian cells, cohesin protein complex is one of the major  players in the establishment of chromatin loops. We present an improved cohesin  HiChIP experimental protocol. Using comprehensive bioinformatic analysis, we show  that a dual chromatin fixation method compared to the standard formaldehyde-only  method, results in a substantially better signal-to-noise ratio, increased ChIP  efficiency and improved detection of chromatin loops and architectural stripes.  Additionally, we propose an automated pipeline called nf-HiChIP (  https://github.com/SFGLab/hichip-nf-pipeline ) for processing HiChIP samples  starting from raw sequencing reads data and ending with a set of significant  chromatin interactions (loops), which allows efficient and timely analysis of  multiple samples in parallel, without requiring additional ChIP-seq experiments.  Finally, using advanced approaches for biophysical modelling and stripe calling  we generate accurate loop extrusion polymer models for a region of interest and  provide a detailed picture of architectural stripes, respectively.", "categories": ["technology development"], "date_created": "2025-03-17T17:15:09.721659+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-03-17T17:23:11.718511+00:00"}, "date_published": "2025-03-14", "public_release": "2025-03-17", "schema_version": "2", "project_release": "2025-03-17", "exp_sets_prod_in_pub": [{"accession": "4DNES7BZ38JT", "status": "released", "@id": "/experiment-set-replicates/4DNES7BZ38JT/", "uuid": "fd3d5eb2-e6b1-434c-9d5e-45926eea696a", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNES7BZ38JT", "experimentset_type": "replicate", "experiments_in_set": [{"@id": "/experiments-chiapet/4DNEX5PBDUFR/", "@type": ["ExperimentChiapet", "Experiment", "Item"], "uuid": "3d9bd66f-077d-417f-86c9-1974bd1a01df", "display_title": "HiChIP against SMC1A protein on HG00731 - 4DNEX5PBDUFR", "status": "released", "experiment_type": {"@id": "/experiment-types/hichip/", "display_title": "HiChIP", "title": "HiChIP", "@type": ["ExperimentType", "Item"], "status": "released", "uuid": "e9e605e9-05f9-41be-a242-92e28f867cae", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiments-chiapet/4DNEXGKZVFJG/", "@type": ["ExperimentChiapet", "Experiment", "Item"], "uuid": "9872b902-6801-417a-8070-fae832c9a883", "display_title": "HiChIP against SMC1A protein on HG00731 - 4DNEXGKZVFJG", "status": "released", "experiment_type": {"@id": "/experiment-types/hichip/", "display_title": "HiChIP", "title": "HiChIP", "@type": ["ExperimentType", "Item"], "status": "released", "uuid": "e9e605e9-05f9-41be-a242-92e28f867cae", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNESOAF3QAA", "status": "released", "@id": "/experiment-set-replicates/4DNESOAF3QAA/", "uuid": "e34f052c-178a-4d92-a846-4d8309f68fc0", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESOAF3QAA", "experimentset_type": "replicate", "experiments_in_set": [{"@id": "/experiments-chiapet/4DNEXABC1PA7/", "@type": ["ExperimentChiapet", "Experiment", "Item"], "uuid": "14859bb4-0f3f-46b7-b40e-1d517a8e21a2", "display_title": "HiChIP against CTCF protein on HG00731 - 4DNEXABC1PA7", "status": "released", "experiment_type": {"@id": "/experiment-types/hichip/", "display_title": "HiChIP", "title": "HiChIP", "@type": ["ExperimentType", "Item"], "status": "released", "uuid": "e9e605e9-05f9-41be-a242-92e28f867cae", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiments-chiapet/4DNEXGDJU4IZ/", "@type": ["ExperimentChiapet", "Experiment", "Item"], "uuid": "589f7ae4-e00e-438f-81e5-154ed361c5ca", "display_title": "HiChIP against CTCF protein on HG00731 - 4DNEXGDJU4IZ", "status": "released", "experiment_type": {"@id": "/experiment-types/hichip/", "display_title": "HiChIP", "title": "HiChIP", "@type": ["ExperimentType", "Item"], "status": "released", "uuid": "e9e605e9-05f9-41be-a242-92e28f867cae", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/publications/b65676d0-556f-4e4e-a8bb-ce0ca10e2d64/", "@type": ["Publication", "Item"], "uuid": "b65676d0-556f-4e4e-a8bb-ce0ca10e2d64", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Buka K et al. 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